-----------------------
Start of variable list:
-----------------------
Sample_ID:
D4-MAA100138-3_56_F-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:44:31 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791079
Current job name : Step_02_D4-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791079.1.linga

Loading required modules...


List files in scratch directory:

total 80M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  40M Oct 12 19:44 SRR6575808_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  40M Oct 12 19:44 SRR6575808_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575808_1.fastq <==
@SRR6575808.1 1/1
GGTTTCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFF
@SRR6575808.2 2/1
CTGTACATAGCTGTTATAGAAGTGGCGATTAGTGTAATTAGTAGGGCTCAGGCGTTGGTGTTGCAGGTATTAATTGCTTCAATAATTAGGTCTTTTGAGT
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575808.3 3/1
GCGGAGATTGAGCTGCGAGCCTGGCGGGCGTGCGCCTAGCCACGTCCCCCCCACCCCCGGGCTCTTCACCCTGATGCTGCACGGGTGCTGAGCCCGTCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFFFFF-FFFFFFFFFFFFFFFFFFFF-F-FFF-FFF--F-FF--FFFF-FF--FF---FF-
@SRR6575808.4 4/1
ACTAGGATTCAGTACAAAATTTGTGTGATTGGGCGGAATATTAGGCTTCGTTGCTTTGAGGTATGAAGGAAAGGTATTAGGGCTAAAATTAGGATAGATA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-F-FFFF-FFFFFFF
@SRR6575808.5 5/1
CTATGAGGCTGGGATCCTGGAAAACCCCAAGAATCAAGCACCTCCGGGTCTCTACACAAAAACTCAGGACCCTGCCAAAGCACCCAACAGCCCAGATGTC
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575808_2.fastq <==
@SRR6575808.1 1/2
NAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTC
+
#F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-F
@SRR6575808.2 2/2
NTCCTACACATCTGTACCCACGCATTCTTCAAAGCTATACTCTTTATATGCTCTGGCTCAATCATTCATAGCCTGGCAGTCGAACAAGACATCCGAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFF8F-
@SRR6575808.3 3/2
AGCTAGAGGAGACCCAGGCTTCCCGACGGATTTCGGTCCAGCCGCTATTGTCAGAGTTCACACAGTAAACACATCGTTCCTCCACCACCATCAGCCGGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F-FFFFFF
@SRR6575808.4 4/2
ATCCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGCTTCTCAGTAGACAAAGCCACCTTGACCCGATTCTTCGCTTTCCACTTCATCTTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575808.5 5/2
GCTCATAGTCGCCCTGCACGTTCATGCTCACCAGCTCTTCATTGTAGAGTGAAAGTGGAGACTCCCGACCGAGGATGTACACTTGGCCCTTGAAGACAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F8FFFFF-FF

Starting FASTQC command


Processing SRR6575808_1.fastq

Printing command:
fastqc --outdir SRR6575808_1.fastq

Analysis complete for SRR6575808_1.fastq

Processing SRR6575808_2.fastq

Printing command:
fastqc --outdir SRR6575808_2.fastq

Analysis complete for SRR6575808_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 425M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 213M Oct 12 19:44 SRR6575808_1.fastq
-rw-r--r--   1 kkarri waxmanlab 213M Oct 12 19:44 SRR6575808_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:16 EDT 2018
0 hours, 0 minutes and 45 seconds elapsed.
==========================================================